I am working on a website with Rmarkdown on gh-pages. However, in R studio you can only create new .Rmd files. This is a problem because I need to convert my .Rmd files into .md files before I push to my github repo.
Does anyone have some advice?
Since you're using RStudio, I'll refer to the documents they provide. Specifically, Markdown Documents, accessible by clicking on the question mark pull-down next to "Knit", select "Using R Markdown" which takes you to their webpage. From there, select "Formats > Markdown".
That page shows you that if you include the following in the YAML (first lines of the document, different kind of meta/markup as markdown), the output will be a .md file:
---
title: "Habits"
author: John Doe
date: March 22, 2005
output: md_document
---
(The only relevant part is the output: portion.) In fact, since you mentioned gh-pages, you may (though not necessarily) want to choose the github-flavor of markdown with this instead:
---
title: "Habits"
author: John Doe
date: March 22, 2005
output:
md_document:
variant: markdown_github
---
From here, click on the "Knit" button and you will get your .Rmd-to-.md conversion.